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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtccgaaaaacatgtgatcgggtgctttaatgaatatgttagtttagattgtttgaatgaccacgatgtcacctgcaaattgacattaattaaactctttttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCA

Basic information

species Physcomitrella patens
transcript PP1S97_78V6.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 3'ss of exon 4
gttggtccgaaaaacatgtgatcgggtgctttaatgaatatgttagtttagattgtttgaatgaccacgatgtcacctgcaaattgacattaattaaactcttt-----ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCA
                                      | ||  | | ||||||||  || |    |   |||||    |   ||     |  |||   ||||      || || ||||||||| ||||| ||||| || ||||||  ||| || ||||||||||| |||||||| ||||||||| |  | ||||| |||||||| || || || ||||
-------------------------------------gtttgc-aatgtagattgtgagatttcatagcttgtcattaactgttttgtgatgcttactttcttcattgcttcaccatagGTGAAAGGTCTGGATGTTGATACTCTTTATGTGTCCCACATTCAAGTTAACCAGGCCCAGAAGCAGAGGCGCCGTACCTACCGTGCTCATGGACGCATCA

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G119169_T04 (Zea mays), 3'ss of exon 3
gttggtccgaaaaacatgtgatcgggtgctttaatgaatatgttagtttagattgtttgaatgacc-acgatgtcacctgcaaattgacattaattaaact--ctttttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCA
                                      | |   | | ||   |   ||   |||| |   |  |  ||| ||  | |   ||||||       || |   ||  |||| || ||||| ||||| || || ||   ||| |||||||||||||| |||||||| |||||||||||  |  | || ||||| || || ||||| ||||
-------------------------------------gtttacaattatactgtccctgtcagacctatctttgcttctgtaatgttatgctaattatgtgagtttctctgctgcagGTAAAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67695151|gb|BJ955384.1|BJ955384
EST:     CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
EST: gi|162259989|gb|FC435292.1|FC435292
EST:     CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
EST: gi|67701215|gb|BJ961448.1|BJ961448
EST:     AGAATGCAGAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: AGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
EST: gi|67704010|gb|BJ964243.1|BJ964243
EST:     CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCANAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
EST: gi|67696219|gb|BJ956452.1|BJ956452
EST:     CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
EST: gi|162276588|gb|FC451971.1|FC451971
EST:     CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
EST: gi|67701414|gb|BJ961647.1|BJ961647
EST:     CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
EST: gi|162252890|gb|FC429263.1|FC429263
EST:     CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
EST: gi|162259990|gb|FC435293.1|FC435293
EST:     CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAG                         GTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC
genomic: CAGCGACATTCTTGTTGGGTTTGTTGAAGAATGCAGAGAGCAATGCAGAGgttggtccga ... ttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaccacgatgtcacctgcaaattgacattaattaaactctttttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCA
                                           ttttgac  putative branch site (score: 3)
                                       ctcttttt  CT-rich tract
                     aaattgacattaatta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtccgaaaaacatgtgatcgggtgctttaatgaatatgttagtttagattgtttgaatgaccacgatgtcacctgcaaattgacattaattaaactctttttgactatagGTGAAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA